The
AiG article attempts to claim that the mitochondrial
evidence is that the Most Recent Common Ancestor of extant humans in the matriarchal
line is 6,500 years old. The AiG article begins with a reasonable definition
of an MRCA (see link for definition)
but then grasps at two relatively recent papers assessing mutational rates in
the mitochondrial DNA and rushes to a prematurely triumphant conclusion about
them.

The Underlying Science

Most of the DNA in the cell of non-bacterial organisms lies in the nucleus.
But in eukaryotes there are structures in the cell outside the
nucleus called the mitochondria. The mitochondria have several functions, the
most obvious of which is that they are responsible for converting 'food' into
energy within the cell. The mitochondria also have their own DNA. (There is
strong evidence that the complex cells of eukaryotes, which are organisms
that have cells with a nucleus, arose originally as a result of parasitism
or symbiosis of one simpler organism with another which developed into what's
called an obligate relationship - that is one in which the different
organisms were so closely bound that they became unable to live without
one another and thence became one organism. But, that's a different
story). (2), (3), (4)

DNA material in the nucleus, in the 46 chromosomes in humans
for example, comes almost equally from the father and mother - 23
chromosomes from each. (I say almost, because the Y chromosome in
mammals is much smaller than the X chromosome). But the mitochondrial
DNA comes only from the mother. This means that the mitochondrial DNA
follows the female line exclusively. If a woman has no daughters, her
mitochondrial DNA (called mtDNA) line dies out.

Nuclear DNA (the 23
pairs of chromosomes in the nucleus) goes through a process called
recombination whereby the chromosomes that are passed on to offspring, say
through the mother, are a mixture of the genes in the mother's parent's
lineage. However the mtDNA is not a mixture like this, but comes exclusively from
the mother. This makes mtDNA a good way to study lineages and to estimate
dates of divergence of different groups. The way this is done is to study
differences between the mtDNA sequences in different individuals. The nature
of the differences provides clues about the relationship between
individuals, and the magnitude of the difference indicates how long ago
the lineages of the two individuals in the maternalline diverged. There are
complications with this process, but that is the basic principle (5)

This is the way that the age of what has been called
mitochodrial Eve is calculated. I don't like the term mitochondrial Eve,
because it implies things that it is not - it is simply misleading. So what is it? It
is properly termed the most recent common (matrilineal) ancestor (MRCA).

That means the most recent individual that lived that stands in the
direct line through mothers with the entire set of individuals in question. If
we are looking at the entire population of people today, the MRCA of that
set is called mitochondrial Eve. The matrilineal MRCA of humans is estimated
to have lived between 150,000 to 200,000 years ago (note that there are
other MRCAs; eg the MRCA as measured by the X-chromosome - since the
X-chromosome descends through fathers and mothers, the lineage is different
- but there is still the concept of the individual from whom the
X-chromosomes of all people alive today descended. That concept is not the same as
matrilineal MRCA or Mitochondrial Eve).

Anyway, the estimate of 150,000
to 200,000 years for matrilineal MRCA was called into question not by one
challenge (as Carl Wieland suggests) but by two challenges. However, Carl Wieland's
implication that it is now considered to be likely that the matrilineal MRCA lived 6,500 years
ago is very misleading.

There are many other
creationist sites which use this research to claim a young (~6,500 year) age for
the origin of humans, and many do so with less care than Wieland. Many
go so far as to say that these papers make it settled question that biblical
Eve existed and that she lived 6500 years ago. Here are a few:

The Challenges to the view
of a 175,000 year date for matrilineal MRCA.

A Challenge which would make the date of matrilineal
MRCA earlier

CHALLENGE 1: In Science 286, 2524 - 2525, Philip Awadalla, Adam
Eyre-Walker, and John Maynard Smith (6) reported evidence of some mixing of
paternal with maternal DNA in the mitochondria. They looked at a measure
called linkage disequilibrium (which determines the degree of 'randomness'
between alleles at different loci) and concluded that there was evidence of
recombination between the father's and mother's mitochondria. This is
radical as it would call a lot of conclusions based on assessing mtDNA into question. This
occurred in 1999. If it were to be true, then it would mean that estimates of
matrilineal MRCA age would be too low, as recombination tends to make DNA
sequences more like one another over time, so it would take longer for the
differences that we observe in people from around the world to evolve.

However,
we soon saw Awadalla et al's study called into question: The following researchers published
direct challenges to the Awadalla et al paper:

Toomas Kivisild and
Richard Villems: "In sum, likely errors in the sequence data used by Awadalla
et al. and the possibility that straightforward phylogenetic explanations
can explain the observed correlations make the conclusions drawn [in the reference below]
weaker than such an exceptionally important problem deserves"

LB Jorde
and M Bamshad: "The possibility of recombination in mtDNA is intriguing and
deserves further evaluation. Six of the eight mtDNA data sets examined here
fail to show a significant decline of LD with physical distance using the r2
statistic, however, and none show a decline using the more appropriate D'
statistic. Thus, LD patterns provide little support for the hypothesis of
mtDNA recombination"

Sudhir Kumar, Philip Hedrick, Thomas Dowling and
Mark Stoneking: "Our reanalysis thus contradicts the contention by Awadalla
et al. (1) that recombination is occurring in human mtDNA. Extensive family
studies have likewise failed to find any exceptions to strict maternal
clonal inheritance of human mtDNA (9-12). There is no need to reconsider
inferences about human or mtDNA evolution that have assumed that
recombination does not occur in human mtDNA."

Thomas J. Parsons and Jodi
A. Irwin: "In light of that finding, it seems unlikely that our understanding
of the pattern and relative rates of sequence evolution within the mtDNA CR
will require substantial revision based on the Awadalla et al. report. Our
analysis also suggests that mtDNA forensic testing will be negligibly
impacted by recombination; forensic applications already deal
successfully with intergenerational mutation [in the references below], clearly a far
more significant effect."

All of these were published in Science 288 p1931 (7). At the
moment this question has not been settled. The bulk of the opinion is that
recombination does not occur, but there has also been some further evidence for
it. Note that if recombination does occur, the matrilineal MRCA of humans
would be OLDER than the current estimate of 150,000 to 200,000
years

.

A Challenge which would make the date of matrilineal
MRCA later

CHALLENGE 2: This is the challenge that Carl
Wieland was referring to.
There have been two papers that have measured unexpectedly high short
term mutational rates in the control region of the mitochondrial DNA.
The control region is a part of the mitochondrial DNA that does not code for
proteins. The normally accepted rate is one mutation every 300 to 600
generations (6000 to 12000 years) and this is calibrated, as Wieland correctly
says, by counting mutations in great ape and human mitochondria and
regressing back to the age of their divergence as determined by fossils
dated by radiometric dating.

(Note the control region is also known as the
D-loop)

The two papers are:

A high observed substitution rate in the
human mitochondrial DNA control region (8):

The rate and pattern of sequence substitutions in the mitochondrial
DNA (mtDNA) control region (CR) is of central importance to studies of
human evolution and to forensic identity testing. Here, we report direct
measurement of the intergenerational substitution rate in the human CR. We
compared DNA sequences of two CR hypervariable segments from close maternal
relatives, from 134 independent mtDNA lineages spanning 327 generational
events. Ten substitutions were observed, resulting in an empirical rate of
1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than
estimates derived from phylogenetic analyses. This disparity cannot be
accounted for simply by substitutions at mutational hot spots,
suggesting additional factors that produce the discrepancy between very
near-term and long-term apparent rates of sequence divergence. The data also
indicate that extremely rapid segregation of CR sequence variants between
generations is common in humans, with a very small mtDNA bottleneck. These
results have implications for forensic applications and studies of human
evolution...

....The observed substitution rate reported here is very high
compared to rates inferred from evolutionary studies. A wide range of CR
substitution rates have been derived from phylogenetic studies, spanning
roughly 0.025-0.26/site/Myr, including confidence intervals. A study
yielding one of the faster estimates gave the substitution rate of the CR
hypervariable regions as 0.118 +- 0.031/site/Myr. Assuming a generation time
of 20 years, this corresponds to ~1/600 generations and an age for the mtDNA
MRCA of 133,000 y.a. Thus, our observation of the substitution rate,
2.5/site/Myr, is roughly 20-fold higher than would be predicted from
phylogenetic analyses. Using our empirical rate to calibrate the mtDNA
molecular clock would result in an age of the mtDNA MRCA of only ~6,500
y.a., clearly incompatible with the known age of modern humans.'

'The rate and pattern of sequence substitutions in the mitochondrial
DNA (mtDNA) control region (CR) is of central importance to studies of
human evolution and to forensic identity testing. Here, we report direct
measurement of the intergenerational substitution rate in the human CR. We
compared DNA sequences of two CR hypervariable segments from close maternal
relatives, from 134 independent mtDNA lineages spanning 327 generational
events. Ten substitutions were observed, resulting in an empirical rate of
1/33 generations, or 2.5/site/Myr. This is roughly twenty-fold higher than
estimates derived from phylogenetic analyses. This disparity cannot be
accounted for simply by substitutions at mutational hot spots,
suggesting additional factors that produce the discrepancy between very
near-term and long-term apparent rates of sequence divergence. The data also
indicate that extremely rapid segregation of CR sequence variants between
generations is common in humans, with a very small mtDNA bottleneck. These
results have implications for forensic applications and studies of human
evolution...

...The observed substitution rate reported here is very high
compared to rates inferred from evolutionary studies. A wide range of CR
substitution rates have been derived from phylogenetic studies, spanning
roughly 0.025-0.26/site/Myr, including confidence intervals. A study
yielding one of the faster estimates gave the substitution rate of the CR
hypervariable regions as 0.118 +- 0.031/site/Myr. Assuming a generation time
of 20 years, this corresponds to ~1/600 generations and an age for the mtDNA
MRCA of 133,000 y.a. Thus, our observation of the substitution rate,
2.5/site/Myr, is toughly 20-fold higher than would be predicted from
phylogenetic analyses. Using our empirical rate to calibrate the mtDNA
molecular clock would result in an age of the mtDNA MRCA of only ~6,500
y.a., clearly incompatible with the known age of modern humans

So it is the
Parsons work that mentions an matrilineal MRCA of 6,500 years that Wieland and
other creationists have latched on to. Note that Parsons says: 'Using our
empirical rate to calibrate the mtDNA molecular clock would result in an age
of the mtDNA MRCA of only ~6,500 y.a., clearly incompatible with the known
age of modern humans'

Both Parsons and Howell use a technique called
restriction fragment length polymorphism (RFLP) analysis. This technique uses
restriction enzymes (enzymes which cut sequences of DNA between short identical
sequences). The length of the cut pieces is analysed and the presence of mutations
will cause the length of the excised sequences to vary. This does tell
us a lot about the different alleles on mitochondrial DNA, but since RFLPs
can be created by events other than single base pair substitutions, it can
be misleading.

Nevertheless, on
the face of it, there is a substantial discrepancy between the mutational or
substitution rates as determined by phylogenetic analysis (comparing the mtDNA
sequences of chimp and human, foe example) and pedigree analysis (data based
on allelic differences between close family members).

Others who attempted to repeat Parson's results
with pedigree data were
unable to do so (10)and derived a rate little different from the
rate given by phylogenetic data which yields an MRCA of 150,000 years. In
order to help resolve these discrepancies, all the scientists have pooled their
data and the result is a mutation rate of one every 1200 years based on the
pedigree data - a rate which is still faster by a factor of five than the
rate given by the phylogenetic approach.

So there is a substantial
issue in how to resolve the rate of mutations in mtDNA, which appear to occur
between one generation and the next, and the much lower rate of mutations that
seem to be fixed after several million years in the genomes of the great apes.
There is a further issue, that the data based on pedigree analysis
of the D-loop gives widely varying mutation rates in different studies.

There is, therefore,
a number of considerations:

We need to
explain the variation in mutational rates in pedigree studies based on analysis
of the D-loop. It is clear that at least some of this variation can
be explained by statistical variations in small samples of a stochastic
process. However, pooling all the data still leads to a 'factor of
five' discrepancy, between the rate measured by pedigree and phylogenetic
studies

We need to
consider whether the mitochondrial DNA does, in fact, mutate at a fixed
rate, and therefore whether it will provide a good 'clock' for dating genomic
events. Furthermore, we must consider whether some parts of the mitochondrial
genome are more 'clock-like' than others.

We need to
consider the fundamental differences between pedigree and phylogenetic studies.
Pedigree studies, particularly those that compare the genetic make-up
of close relatives, measure a rate of mutation from one generation to the
next Phylogenetic studies, or pedigree studies that compare broad
populations that have been in existence for many generations will yield
a rate of fixed mutations or permanent substitutions in that lineage's
genome. These rates might be different, because mildly deleterious mutations
will be eliminated over time from the gene pool, and because in some cases,
a particular mutation might mutate back to the original sequence

We need to
consider the possibility that mitochondrial mutations usually occur
in some, but not all, of the thousands of copies of mitochondrial DNA
present in each cell. Such a condition is called mitochondrial heteroplasmy,
and, if it occurs in the germ line, can result in tissue mosaicism (different
mitochondrial DNA in different tissues). It is frequently deleterious

We need to
consider whether restriction fragment length polymorphism analysis (RFLP)
is a good technique for estimation of mutation rate

Discussion

It has been shown
by Hasegawa et al (11)that
the non-synonymous to synonymous rate ratio of mitochondrial polymorphisms
is much higher within species than between species. What does this mean? Synonymous
mutations make no difference to the protein encoded and therefore are not acted
on by natural selection. Synonymous mutations are therefore neutral and
their incidence in the population depends on the population dynamics of the lineage
possessing them. Non-synonymous mutations do cause changes in protein, and
the probability of their survival over many generations depends on whether they
are deleterious, neutral or beneficial. Since most mutations are deleterious,
the ratio of non-synonymous to synonymous mutations is less than one. In
fact the study found that the ratio within primate species varies from five
to 10 times the ratio between species. (Human ratio = 0.2, chimpanzee
= 0.5, gorilla = 0.4, between species = 0.033 - 0.04). Hasegawa et al
conclude that this is due to the elimination of slightly deleterious mutations
from the population. Since synonymous rates have no effect on the phenotype,
they are expected to be the broadly the same rate across all primate species.
Differences in the ratio are therefore to be explained by differences
in the fixing of non-synonymous mutations over time. Hasegawa et al also
note that the D-loop is functional and that the high mutational rate obtained
in pedigree analyses is because more deleterious mutations are observed in this
type of study, compared with long term phylogenetic studies, where deleterious
mutations would be expected to be eliminated over time.

Using close
relatives in sequential generations to estimate the long term rate of fixed
substitutions

The use of
RFLP analysis for this purpose

Ingman et al point out that there is a big variation in mutational
rates on the control region or D-loop, for different populations. They point
out that the mutational rate of the mitochondrial genome, excluding the
D-loop, has evolved at a constant rate in humans, and, by analysing data across
primate species, and using gorilla as an out-group, they demonstrate that there
is no significant difference between the evolutionary rate of human and chimpanzee
mtDNA, excluding the D-loop. Hence they specifically exclude the
D-loop from their analysis.

Ingman et al study
a representative sample of the human population. They analyse the complete
mtDNA of 53 humans of diverse origins. They also use a technique for sequencing using specific
PCR primers and direct sequencing chemistry (specifically BigDye from Applied
Biosystems) to sequence the entire mitochondrial genome (as opposed to
looking at RFLPs). By comparing the variation within the human population with
the difference between human and chimpanzee mtDNA, they obtain a
mutational rate across the whole mitochondrial genome, excluding the D-loop, of
1.7x10-8 mutations per site per year.

On the basis of the humans in this study with the
greatest difference in their mitochondrial DNA, the authors say
that: 'The age of the most recent common ancestor (MRCA) for mtDNA, on the
basis of the maximum distance between two humans (5.82 x 10-3
substitutions per site between the Africans Mkamba and San), is
estimated to be 171,500 ± 50,000 yr BP'.

So the most recent study
using the most appropriate techniques confirm the date of matrilineal MRCA at
between 150,000 and 200,000 years.

A similar exercise has also been
performed on the Xq13.3 region of the X-chromosome of the same individuals
used in this study by Kaessmann et al (13).

The X-chromosome is
the female sex chromosome in the nucleus, but because it is 'paired' with
the tiny male Y-chromosome, it mostly doesn't recombine and is similar to
mitochondrial DNA in that respect; but it is passed on by both fathers
and mothers to offspring and so is different from mitochondrial DNA in that
respect. Because the effective population size of the X-chromosome is three
times that of mitochondrial DNA, the X-chromosome MRCA is predicted to be
three times older than the matrilineal or mitochondrial MRCA. The age of
the MRCA of Xq13.3 is found to be in agreement with the mtDNA data (mtDNA
MRCA age: 171,500 years BP;
Xq13.3 MRCA age: 479,000 years BP)

Ingman et al conclude:'Our results
indicate that the field of mitochondrial population genomics will provide a
rich source of genetic information for evolutionary studies. Nevertheless,
mtDNA is only one locus and only reflects the genetic history of females.
For a balanced view, a combination of genetic systems is required. With the
human genome project reaching fruition, the ease by which such data may be
generated will increase, providing us with an evermore detailed
understanding of our genetic history.'

Conclusion

No-one in the science
community thought that the Parsons et al study supported a matrilineal MRCA
of 6,500 years. Nevertheless their work did result in discrepancies between
the known date of human geographic dispersion (at least 60,000 years BP) and
the apparently very high rate of mitochondrial mutation, which, if taken at face
value, would yield a matrilineal MRCA 6,500 years ago.

Subsequent studies
have shown the following:

RFLP analysis
(as used by Parsons et al and Howell et al) is not a an appropriate
approach to determine mutational rates; whole genome sequencing as used
by Ingman et al is more accurate

There is considerable
disagreement between different studies of mutational rate, as measured by
pedigree analysis of near relatives, concentrating on the D-loop

Some of this
variation is simply the result of stochastic variations in small sample
sizes

Much of this
variation is due to genuinely different mutational rates on the D-loop in
different populations

The rate of
fixed mutations over many generations is much lower than the instantaneous
mutational rate from generation to generation as a consequence of the elimination
of slightly deleterious mutations from the gene pool

The presence
of mitochondrial heteroplasmy will result in an elevated mutational
rate in pedigree studies

The fixed mutational
rate outside the D-loop over many generations is constant across primate
species and can be used as an accurate mutational 'clock'

A study
of a representative sample of humans from the worldwide population using
whole genome analysis and excluding the D-loop yields an age for matrilineal
MRCA (Mitochondrial Eve) of 150,000 to 200,000 years

The same humans
give an X-chromosome MRCA of ~480,000 years as predicted.

It seems to be the
nature of creationist apologists to misrepresent and misuse scientific work.
The fact that so many creationists and creationist websites latch on to
the Parsons et al paper ,and claim that it is proof for a biblical Eve living
6500 years ago, (even though Parsons et al claim no such thing), demonstrates
two things:

They do not
understand or they deliberately misrepresent the concept of the matrilineal
Most Recent Common Ancestor which does not point to the only female
human ancestor

They
ignore the fact that subsequent research has largely resolved the issues
that the Parsons et al paper raised.

It is my confident
prediction that both ill-informed creationists and those who should know better will be
using this discredited argument 20 years from now. They will be as wrong
then as they are now.

____________________________________________________________

Wieland
replied to this article in 2005. My response to his reply is here.
(October 2006)